Commercial shrimp farms suffer extensive losses due to the effects of a number of common pathogens. Infectious Hypodermal and Hematopoietic Necrosis Virus (IHHNV) is one of the most serious viral pathogens of farmed penaeid shrimp. It is widely distributed in many countries and has a large range of hosts. For example, IHHNV causes mass mortality among the Western blue shrimp (Penaeus stylirostris) and severe deformation in the Pacific white shrimp (Penaeus vannamei). IHHNV is a small, single stranded DNA-containing parvovirus, the complete genome of which has been sequenced (Bonami et al., J. Gen. Virology 71 (Pt 11):657-2664 (1990); GenBank AF218266).
IHHNV is extremely detrimental to the shrimp farming industry, being responsible for catastrophic epidemics worldwide. Detection of IHHNV in hatchery broodstock and in post-larvae allows infected shrimp to be eliminated before entry into a commercial production system. Consequently, a variety of methods have been developed for the detection of IHHNV in shrimp, including nucleic acid-based methods and immunological methods (Lightner et al., Aquaculture 164(1):201-220 (1998)). Nucleic acid amplification methods such as polymerase chain reaction (PCR) and isothermal amplification are of particular interest because they are simple, rapid, and sensitive. PCR methods for the detection of IHHNV, which are based on amplifying different diagnostic regions of the genome, have been described (see for example Nunan et al., Mar. Biotechnol. 2(4):319-328 (2000); Yue et al., J. AOAC International 89(1):240-244 (2006); Tang et al. Dis. Aquat. Org. 44(2):79-85 (2001); Hu et al., CN 1410549; and Dhar et al. J. Clin. Microbiol. 39(8):2835-2845 (2001)). Additionally, a loop mediated isothermal method for the detection of IHHNV is described by Sun et al. (J. Virol. Methods 131(1):41-46 (2006)).
All of the above methods are useful for the detection of IHHNV; however, they generally suffer from a lack of specificity, sensitivity, or are complex and time consuming. Additionally, because of the high gene mutation rate in the virus, tests directed to different regions of the genome would be useful. Therefore, there is a need for a highly sensitive assay for IHHNV that is rapid, accurate and easily used in the field. The stated problem is addressed herein by the discovery of primers based on new portions of the IHHNV genome. The primers identified herein can be used in primer directed amplification or nucleic acid hybridization assay methods for the detection of IHHNV without the problems associated with previous methodologies.